InDesign section weirdness

I'm currently typesetting a book in InDesign CS4. The book has footnotes at the bottom of almost every page. The footnotes are linked to reference numbers in the main text. By 'linked', I mean physically linked, so if the reference moves to the next page, the footnote follows it.

OK, all I'm trying to do is make the footnote numbering start again from 1 with each chapter, and so far, so good. I'm making each chapter a new section, and the footnotes are automatically updating to the new numbering.

Until now. Suddenly, I've come to one spread, p134 is the end of one chapter, and p.135 is the start of another. At the bottom of p134 is a footnote numbered 29. There are two footnotes at the bottom of p135, currently numbered 30 and 31. Placing a section marker at the top of p135 SHOULD automatically change footnotes 30 and 31 into 1 and 2. BUT, what's actually happening is that footnote 29 on the previous page is changing to 1, while the footnotes on page 135 are changing to 2 and 3. Why on earth is this happening???? And more importantly, what can I do to correct it?